/tools

This repository provides a PyMOL extension that allows users to color protein structures derived from the AlphaFold Protein Structure Database according to their confidence levels (pLDDT). It enhances the visualization of protein structures, aiding in the analysis of structural biology data.

The 'molecules.js' library is designed for chemical graph theory applications in JavaScript. It enables users to import molecules, compute graph matrices, and visualize molecular structures, making it a useful tool for cheminformatics and molecular property analysis.

r3dmol is an R package that enables users to visualize molecular data in three dimensions using the 3Dmol.js library. It supports various molecular structures and allows for interactive manipulation and styling of the visualized models.

DuIvyTools is a Python library that facilitates the analysis and visualization of molecular dynamics simulation results from GROMACS. It offers various commands for processing data files, making it a useful tool for researchers in computational chemistry.

xyz2graph is a Python package that converts XYZ molecular files into interactive 3D visualizations and NetworkX graphs. It allows users to analyze molecular structures and visualize them effectively.

VisualFactory is a collection of scripts designed for high-quality 3D molecular visualization within the ChimeraX environment. It allows users to create detailed and scientifically accurate representations of molecular structures and dynamics, enhancing the understanding of molecular interactions.

ElectronVisualized is a web-based interactive tool that visualizes atomic and molecular orbitals in quantum mechanics. It allows users to draw molecules and explore their properties, making it a useful resource for those studying chemistry and molecular structures.

Atomify enables real-time molecular dynamics simulations in the browser using LAMMPS, providing users with the ability to visualize simulations and analyze physical quantities in real-time. It simplifies the workflow for molecular dynamics by integrating simulation and visualization into a single platform accessible via a web interface.

Pizza.py is a collection of Python tools designed to facilitate pre- and post-processing for the LAMMPS molecular dynamics package. It includes functionalities for creating input files, converting file formats, processing simulation data, and visualizing results.

Molecule3d is a React component that wraps 3Dmol.js to visualize molecular structures in three dimensions. It allows users to input molecular data and customize the visualization, making it a useful tool for molecular representation.

py2Dmol is a Python library designed for visualizing protein, DNA, and RNA structures in 2D, suitable for use in Google Colab and Jupyter notebooks. It allows users to load and display molecular structures interactively, making it a useful tool for molecular representation.

The Cheminformatics Microservice offers essential microservices for cheminformatics, including molecular property calculations, structure validation, and visualization through an API. It supports various chemical formats and provides tools for chemical analysis and natural product scoring.

DuIvy provides scripts for the analysis and visualization of molecular dynamics simulations. It also includes tutorials that may assist users in understanding and applying these tools effectively.

Chemkit is an open source C++ library that facilitates molecular modeling and cheminformatics, providing tools for molecular visualization. It aims to support various applications in the field of chemistry through its comprehensive library functionalities.

LifeBrush is a VR toolkit that allows users to create and simulate biomolecular environments using a generative brush for painting molecular structures. It employs an agent-based modeling framework to visualize and interact with molecular dynamics in a 3D space.

Chemistry Drawer is a Python package that allows users to draw and visualize molecular structures using Plotly. It provides customizable aesthetics for atoms, bonds, and rings, making it a useful tool for representing chemical structures.

RMD_Digging is a toolkit designed for pre-processing and post-processing tasks in reactive molecular dynamics simulations using the ReaxFF force field. It includes functionalities for data extraction, statistical analysis, and visualization of molecular structures and trajectories.

The ipymolstar repository offers a Jupyter Notebook-based tool for visualizing and analyzing molecular structures using the Mol* framework. It allows users to interact with molecular data, including loading and displaying structures, which is essential for molecular biology and computational chemistry applications.

PyVibMS is a PyMOL plugin that allows users to visualize vibrations in molecules and solids. It supports various quantum chemistry programs and provides tools for analyzing vibrational spectra, making it useful for researchers in computational chemistry.

The Pharmacophore-Toolkit allows users to generate simple pharmacophore models using RDKit, which can be derived from crystal structures, docking poses, or SMILES strings. It provides functionalities for visualizing these models in both 2D and 3D formats, aiding in the understanding of molecular interactions.

MolecuLarva is a molecular simulation tool that visualizes the behavior of particles in 2D and 3D space, simulating interactions such as collisions and forces between different particle types. It aims to study self-organizing systems and explore conditions for the emergence of artificial life.

MolScript is a program that produces publication-quality images of macromolecular 3D structures, such as proteins, in both schematic and detailed representations. It has been a standard tool in the science of macromolecular structures for many years.

Molecular Blender is a Blender plugin that specializes in importing and visualizing molecular data from .xyz files, enabling users to create animations and representations of molecular structures. It supports various visualization styles and can dynamically represent molecular properties such as atomic charges and molecular orbitals.

The GenUI framework offers a backend for molecular generation and QSAR modeling through a REST API, enabling users to manage datasets and visualize chemical spaces. It supports the integration of various molecular generators and facilitates the upload and download of bioactivity datasets.